library(xcms)
## Loading required package: mzR
## Loading required package: Rcpp
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
##
## IQR, mad, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, cbind, colnames,
## do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff,
## sort, table, tapply, union, unique, unsplit, which, which.max,
## which.min
## Loading required package: ProtGenerics
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
library(faahKO)
library(ggplot2)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:xcms':
##
## groups
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(reshape2)
cdfpath <- system.file("cdf", package = "faahKO")
cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
xr<-xcmsRaw(cdffiles[1])
xr
## An "xcmsRaw" object with 1278 mass spectra
##
## Time range: 2501.4-4499.8 seconds (41.7-75 minutes)
## Mass range: 200-600 m/z
## Intensity range: 70-1373180
##
## MSn data on 0 mass(es)
## with 0 MSn spectra
## Profile method: bin
## Profile step: 1 m/z (401 grid points from 200 to 600 m/z)
##
## Memory usage: 10.7 MB
plotTIC(xr)
xr@tic
## [1] 948152 954658 950875 943870 949634 965587 968803 964557
## [9] 969358 964664 971634 971365 974217 978026 970441 972351
## [17] 967410 961510 965924 961907 965915 965538 960962 962236
## [25] 963604 963342 965389 955182 947886 945688 947762 949261
## [33] 950104 950831 943956 942093 944989 941028 930184 923923
## [41] 922735 922978 920220 919034 926627 932312 939707 939193
## [49] 950585 988887 1012947 1052623 1089801 1121788 1153565 1182374
## [57] 1203382 1213689 1206138 1192362 1179480 1168073 1159887 1143179
## [65] 1130904 1108635 1090106 1079381 1073463 1063551 1056777 1058043
## [73] 1048315 1029606 1016288 1012317 1010362 1008342 1007927 1001495
## [81] 994241 991321 995081 1000696 1006012 1010445 1010192 1000548
## [89] 1000251 1013063 1035840 1068247 1131977 1211678 1323509 1454893
## [97] 1596095 1726614 1845832 1929584 1975660 1990756 1983879 1981681
## [105] 1981225 2001352 2076263 2184020 2337732 2489592 2616192 2699532
## [113] 2776014 2845992 2879776 2864635 2814306 2747112 2670893 2576134
## [121] 2466354 2332135 2195738 2060420 1934017 1820978 1704743 1598196
## [129] 1495144 1413206 1354217 1307148 1273195 1236117 1197277 1164971
## [137] 1153781 1141773 1132081 1126910 1107519 1104597 1094940 1090685
## [145] 1082949 1078664 1065321 1056660 1053121 1055837 1062535 1082841
## [153] 1108271 1148762 1180745 1216048 1242786 1266753 1278982 1281879
## [161] 1273977 1261918 1236184 1209667 1191196 1168379 1153621 1134224
## [169] 1115367 1111315 1141234 1200931 1301340 1452604 1638248 1848593
## [177] 2064119 2243219 2393347 2484020 2538763 2574788 2568901 2511377
## [185] 2427208 2319780 2187203 2058017 1921906 1798203 1678016 1562513
## [193] 1461224 1378079 1318078 1269855 1222825 1200244 1182833 1165732
## [201] 1158537 1164549 1165669 1169317 1185052 1195401 1205060 1215649
## [209] 1226407 1223247 1213606 1221738 1229800 1232470 1237469 1242425
## [217] 1246680 1240525 1235645 1238741 1247128 1247666 1249171 1257258
## [225] 1270229 1296567 1318313 1336171 1333280 1345191 1358078 1379915
## [233] 1397397 1410733 1407732 1418112 1443059 1452214 1457244 1465325
## [241] 1471362 1458500 1461502 1480420 1488575 1474581 1487778 1486055
## [249] 1486331 1492078 1502957 1510785 1516092 1529547 1540462 1545746
## [257] 1545159 1540285 1559794 1573836 1595906 1621487 1634816 1668121
## [265] 1685742 1719225 1741881 1755954 1769490 1774350 1791580 1784915
## [273] 1771809 1746439 1728918 1704181 1699212 1665394 1650910 1637394
## [281] 1607237 1591654 1592812 1594733 1591871 1587330 1577106 1568270
## [289] 1564406 1569054 1566882 1573750 1557696 1546669 1548667 1552492
## [297] 1542310 1529498 1518640 1507836 1500306 1499182 1487030 1470177
## [305] 1462480 1449739 1452404 1445392 1439811 1440987 1433821 1425530
## [313] 1417061 1414153 1418914 1430596 1435735 1437346 1445789 1431984
## [321] 1435822 1446139 1440606 1439012 1426008 1431290 1432261 1431220
## [329] 1419388 1416158 1410527 1410297 1421765 1423667 1424063 1410890
## [337] 1398731 1384351 1369588 1362710 1347777 1337880 1322352 1318862
## [345] 1306935 1306680 1310284 1313143 1316656 1324811 1340222 1350161
## [353] 1368371 1383146 1409618 1420724 1447455 1466349 1474997 1472526
## [361] 1475258 1467224 1466553 1452237 1434372 1418788 1414168 1408275
## [369] 1390868 1380443 1370014 1356349 1351401 1347061 1335776 1329321
## [377] 1321528 1320879 1319415 1317767 1315184 1305109 1293650 1291085
## [385] 1289964 1287638 1289619 1280679 1267864 1269163 1264599 1272310
## [393] 1267168 1266685 1269294 1270465 1270621 1264610 1264432 1272707
## [401] 1274919 1265394 1265655 1268532 1273274 1275777 1285020 1295752
## [409] 1327596 1387673 1489675 1672065 1925216 2220211 2561554 2899077
## [417] 3183572 3399013 3534682 3655550 3744633 3792791 3799214 3770414
## [425] 3734659 3690353 3620137 3525887 3427586 3353456 3282923 3194111
## [433] 3112582 3050411 2977495 2903657 2832837 2767536 2705990 2653695
## [441] 2585103 2515463 2435910 2363101 2302676 2246279 2198579 2142911
## [449] 2091944 2032856 1988677 1966529 1933520 1910040 1888659 1871381
## [457] 1862669 1844917 1846045 1839911 1836259 1851901 1873614 1896584
## [465] 1902852 1906842 1908996 1911053 1913476 1924928 1940186 1970999
## [473] 2003220 2057184 2086397 2131621 2159541 2175560 2180855 2188392
## [481] 2156315 2118394 2086059 2061342 2048114 2046219 2057868 2110345
## [489] 2188315 2300619 2409399 2503341 2578732 2623811 2644581 2647912
## [497] 2643534 2633881 2615308 2583191 2566776 2578897 2637474 2725487
## [505] 2856667 3009459 3180441 3383663 3581645 3771287 3935906 4077654
## [513] 4189880 4257108 4289336 4326073 4363576 4399575 4420037 4416479
## [521] 4409271 4402916 4363976 4296614 4189189 4089764 4004224 3936341
## [529] 3906573 3932152 3978812 4086272 4216894 4355958 4469479 4547873
## [537] 4607500 4634347 4625075 4599847 4546050 4464662 4340748 4198104
## [545] 4063318 3941792 3824316 3704788 3585367 3460679 3344363 3253713
## [553] 3199488 3205174 3272527 3391207 3552053 3710168 3853115 3946218
## [561] 4009762 4066949 4125008 4164565 4173423 4164368 4149586 4105863
## [569] 4042014 3982422 3943186 3889747 3833539 3787667 3750715 3737703
## [577] 3698772 3647732 3612343 3576120 3532291 3475672 3421787 3345433
## [585] 3266252 3196057 3120181 3042148 2956991 2889870 2830928 2792445
## [593] 2758923 2731737 2712933 2704960 2702942 2719255 2744317 2786846
## [601] 2837578 2889492 2905602 2940953 2971147 3022174 3039224 3044218
## [609] 3043948 3021154 2986846 2960530 2931693 2905957 2858470 2827817
## [617] 2777815 2743104 2717679 2706667 2692890 2673893 2649744 2623651
## [625] 2604775 2580190 2576467 2573832 2567970 2576394 2634331 2663412
## [633] 2673523 2725807 2780814 2841104 2891148 2994116 3149356 3356068
## [641] 3558091 3730448 3876774 4008499 4100065 4137212 4146445 4155521
## [649] 4144890 4126892 4117441 4102312 4075047 4039427 4029589 4000364
## [657] 3941099 3864471 3809498 3765761 3715432 3644832 3562377 3471036
## [665] 3397884 3305360 3229110 3163499 3102655 3064961 3021848 2988678
## [673] 2967299 2954219 2943733 2929211 2918452 2914277 2918752 2929288
## [681] 2954290 2980152 3003550 3027383 3039737 3052933 3069215 3092545
## [689] 3111335 3119313 3126802 3131407 3124690 3111021 3099996 3083754
## [697] 3062884 3029085 2992268 2968817 2940242 2908796 2891124 2875096
## [705] 2872865 2894915 2922161 2956186 3020915 3102843 3197869 3292958
## [713] 3358219 3410276 3425282 3404298 3360022 3306175 3244718 3188587
## [721] 3137269 3110965 3098542 3106617 3104778 3105047 3098997 3110945
## [729] 3154823 3207575 3288710 3377831 3493514 3622504 3747468 3884041
## [737] 4030853 4117974 4216706 4297713 4319800 4340639 4300571 4228095
## [745] 4112744 3967090 3851069 3726901 3598253 3514926 3421937 3344681
## [753] 3247316 3141637 3072042 3010917 2981364 2931631 2872730 2856452
## [761] 2826274 2811758 2826135 2853480 2829714 2811595 2810306 2792254
## [769] 2775147 2730241 2688709 2653496 2597134 2541317 2493747 2423760
## [777] 2369627 2315660 2271354 2244406 2208706 2165758 2131858 2084505
## [785] 2034466 1994813 1959685 1945968 1943996 1952187 1955029 1954597
## [793] 1952869 1951186 1949962 1945740 1935313 1921166 1910021 1902289
## [801] 1886374 1857205 1830948 1791583 1760211 1732374 1706762 1689288
## [809] 1669498 1670197 1680873 1681462 1688099 1694698 1701549 1732812
## [817] 1770348 1795806 1798572 1795862 1788219 1787413 1782621 1779583
## [825] 1767634 1749198 1713618 1688633 1673848 1680083 1683670 1698949
## [833] 1726022 1758340 1802901 1862555 1923836 1991965 2070876 2148028
## [841] 2217256 2274495 2307085 2319059 2318841 2313629 2313652 2323478
## [849] 2339036 2352273 2357951 2347212 2323504 2294203 2265035 2233822
## [857] 2197123 2164606 2136143 2108040 2085426 2076345 2078273 2099248
## [865] 2127957 2162242 2190449 2212008 2220029 2200050 2161932 2124233
## [873] 2120693 2143089 2178083 2213169 2239546 2251881 2253806 2257554
## [881] 2268315 2265459 2259565 2258278 2264114 2250350 2207695 2152133
## [889] 2119813 2105645 2103384 2107703 2087565 2049436 2026100 2034285
## [897] 2057817 2075273 2075565 2058579 2051116 2052822 2033323 2011625
## [905] 2013490 2035047 2041788 2028113 2014793 2011168 2012942 2012433
## [913] 1999993 1973221 1949842 1939031 1936301 1926400 1922731 1908002
## [921] 1889714 1859886 1838434 1819283 1804334 1798277 1802582 1793352
## [929] 1786508 1763553 1759723 1750716 1737732 1735163 1742355 1744645
## [937] 1748562 1746883 1761666 1775387 1788628 1786130 1785323 1799774
## [945] 1811834 1811051 1802536 1794056 1784788 1786431 1765935 1749149
## [953] 1743696 1744057 1747921 1734278 1722104 1715808 1709440 1703933
## [961] 1694451 1686106 1683122 1681523 1679190 1672262 1669629 1670130
## [969] 1673267 1680515 1691405 1700136 1712220 1711876 1706183 1701413
## [977] 1710983 1719643 1726023 1718751 1716108 1729049 1752903 1782874
## [985] 1814469 1844167 1885509 1947868 2026755 2114460 2212317 2322109
## [993] 2441848 2545429 2610041 2633552 2637636 2646454 2661609 2666096
## [1001] 2650359 2636007 2623724 2616778 2604329 2593868 2576468 2570849
## [1009] 2577175 2596545 2631177 2672064 2709265 2739385 2770737 2787060
## [1017] 2791674 2784402 2773129 2754182 2728527 2689325 2651845 2617581
## [1025] 2595398 2589494 2612409 2668643 2755068 2849776 2935145 2994745
## [1033] 3024610 3041911 3032605 3011983 2971748 2911739 2832265 2747687
## [1041] 2660795 2583417 2499426 2383636 2221057 2011419 1785047 1576868
## [1049] 1389995 1227663 1092690 990658 917890 862065 827533 822187
## [1057] 838078 874708 921570 971302 1023679 1087242 1161856 1231503
## [1065] 1268068 1278065 1283304 1274596 1239646 1179942 1089704 992996
## [1073] 901869 839908 806691 790456 788429 798808 822139 851122
## [1081] 882609 917075 959708 1002758 1038929 1063770 1066993 1043521
## [1089] 997989 941175 887703 846285 820738 802354 772209 727521
## [1097] 666423 602503 536473 471709 411447 358031 313912 279419
## [1105] 249921 223292 200642 182122 165472 151513 133247 125548
## [1113] 125039 128482 136752 146306 158895 171257 178195 183319
## [1121] 187803 189321 185411 179032 173595 168559 165674 163804
## [1129] 164210 169931 176851 184991 202139 237677 290975 347405
## [1137] 397625 441460 478102 505237 519291 520032 502132 474585
## [1145] 439033 403486 367058 332441 299054 271361 250329 237356
## [1153] 229807 229676 232399 241681 246510 250882 248035 240336
## [1161] 228821 213726 199433 185132 174501 167658 163386 162052
## [1169] 161110 160466 163481 164364 167038 170323 174543 180619
## [1177] 187405 195565 201388 203701 207552 214127 220112 224087
## [1185] 229035 235994 241153 243508 245877 248773 251631 254062
## [1193] 253961 251228 248855 252043 258329 264652 267781 269081
## [1201] 270533 274900 278317 279322 281004 285454 289244 292366
## [1209] 293802 298774 310358 324547 335360 340057 350054 367446
## [1217] 388942 411148 436543 464298 495407 522991 542339 559298
## [1225] 581797 610969 637940 658849 661923 657429 648016 640075
## [1233] 631756 625106 621901 615456 606095 595305 587658 580470
## [1241] 583166 595588 614471 633097 651229 665310 683337 708157
## [1249] 737405 763035 780251 790361 794650 792521 785598 768734
## [1257] 752433 724891 698871 669392 643353 615424 584725 563652
## [1265] 547730 531399 518629 504554 494902 488970 482959 476756
## [1273] 472473 466554 464119 469922 483393 499115
plot(xr@scantime,xr@tic)
plot(xr@scantime,xr@tic, type = 'l')
retention_time_ms<-xr@scantime
total_ion_chromatogram<-xr@tic
chrom <- data.frame(retention_time_ms,total_ion_chromatogram)
write.csv(chrom, 'chrom.csv', row.names = FALSE)
gg_chrom<-ggplot(chrom, aes(chrom$retention_time_ms)) +
geom_line(aes(y = chrom$total_ion_chromatogram))
gg_chrom
ggplotly(gg_chrom)
spec<-read.csv('chrom.csv',header = T)
gg_chrom<-ggplot(spec, aes(spec$retention_time_ms)) +
geom_line(aes(y = spec$total_ion_chromatogram))
library(dygraphs)
dygraph(spec) %>%
dyRangeSelector()